Fig. 7
Differences in the ileal metabolome and short-chain fatty acids of broiler chickens with cages and ground litter floor pens. PLS-DA scatter plot for GC group vs. CC group on d 31 (A, B). Permutation test (C) of PLS-DA model for group GC versus CC (negative ion mode). Volcano plot for group GC versus CC (D, E). Each point in the mountain chart represents a metabolite, the abscissa represents the fold change (take the log2 logarithm) of each substance in the group, and the ordinate represents the P-value of the t-test (take the log10 logarithm). The size of the scatter points represents the VIP value of the PLS-DA model, and the larger the scatter point, the greater the VIP value. Scattered colors represent the final screening results. Significantly up-regulated metabolites are shown in red, significantly down-regulated metabolites are shown in green, and non-significantly different metabolites are shown in grey. GC group versus CC group KEGG pathway enrichment analysis bubble chart (F, G). According to the results of KEGG enrichment, select the top 20 pathways sorted by P-values from small to large to draw a bubble chart. The abscissa is x/y (the number of differential metabolites in the corresponding metabolic pathway/the total number of metabolites identified in the pathway), the larger the value, the higher the enrichment of differential metabolites in the pathway, and the ordinate is the KEGG pathway name. The ordinate and color of the bubble indicate the P-values of the enrichment analysis (take the negative common logarithm, ie –log10 P-values). The redder the color, the smaller the P-values, indicating that the degree of enrichment is more significant, the reliability of the test is greater and the difference in statistics is more significant. The size of the dot represents the number of different metabolites in the corresponding pathway. The larger the dot, the more differential metabolites in the pathway. The levels of short-chain fatty acids (H-J) in the ileal contents of broiler chickens were analyzed by high performance liquid chromatography (Dionex, USA). All graphs are presented as mean, with the standard deviation (SD) shown via the whiskers. Statistical differences were determined by one-way ANOVA, with the P values for the main effects written out below each plot. P-values represent the effect of the rearing system. GC/Litter: ground litter control group, CC/Cage: cage control group